Changes in population structure of the soilborne fungus Gaeumannomyces graminis var. tritici during continuous wheat cropping

A method was developed to assess the genetic structure of Gaeumannomyces graminis var. tritici (Ggt) populations and test the hypothesis of an association between disease level in the field with changes in pathogen populations. A long-term wheat monoculture experiment, established since 1994, generated different take-all epidemics with varying the number of wheat crop successions in the 1999-2000 cropping season. Genetic polymorphism in Ggt populations was investigated over natural, local epidemics. Four populations of 30 isolates were isolated from necrotic wheat roots in a first, third, fourth, and sixth wheat crop in the same year. Each Ggt isolate was characterized with RAPD (Random Amplification Polymorphism DNA) markers and AFLP (Amplified Fragment Length Polymorphism) fingerprinting. Seventeen multilocus genotypes based on the combination of RAPD and AFLP markers were identified among all these populations. The 120 isolates were divided into two main groups, G1 and G2, according to bootstrap values higher than 86%, except for an unique isolate from the third wheat crop. Within each group, populations ranged between 93 and 100% similarity. Both groups included isolates collected from the first, third, fourth or sixth wheat crop. However, G1 group profiles dominated amongst isolates sampled in the first and the sixth wheat crops, whereas G2 group profiles largely dominated amongst isolates collected from the third and fourth wheat crops. Aggressiveness of group G2 (38%) was significantly greater than that of G1 (29.5%). These results suggest that changes in Ggt population structure occur during continuous wheat cropping. The distinction of two Ggt groups provides a simple basis for further spatio-temporal analysis of Ggt population during polyetic take-all decline.     

Occurrence of Phialophora radicicola var. graminicola and Gaeumannomyces graminis var. tritici on roots of wheat in field crops

Assessments of Phialophora radicicola var. graminicola (PRG) and Gaeumannomyces graminis var. tritici (GGT) were made by culturing and by direct microscopic examination of pieces of seminal roots from 16 winter wheat crops grown in different cropping sequences and with different phosphate manuring. PRG occurred on all wheat crops, but was abundant only on wheat after grass, where it seemed to delay the onset of damaging take-all by 1 yr. Delayed occurrence of take-all by phosphate fertiliser was not related to differences in populations of PRG. Wheat grown in ‘take-all decline’ soils had only small amounts of PRG, indicating that the development and the decline of take-all epidemics may be influenced by different biological control mechanisms; breaking sequences of wheat crops by 1 yr grass leys might harness the advantages of both mechanisms.     

Control of Mn status and infection rate by genotype of both host and pathogen in the wheat take-all interaction

Take-all is a world-wide root-rotting disease of cereals. The causal organism of take-all of wheat is the soil-borne fungus Gaeumannomyces graminis var tritici (Ggt). No resistance to take-all, worthy of inclusion in a plant breeding programme, has been discovered in wheat but the severity of take-all is increased in host plants whose tissues are deficient for manganese (Mn). Take-all of wheat will be decreased by all techniques which lift Mn concentrations in shoots and roots of Mn-deficient hosts to adequate levels. Wheat seedlings were grown in a Mn-deficient calcareous sand in small pots and inoculated with four field isolates of Ggt. Infection by three virulent isolates was increased under conditions which were Mn deficient for the wheat host but infection by a weakly virulent isolate, already low, was further decreased. Only the three virulent isolates caused visible oxidation of Mn in vitro. The sensitivity of Ggt isolates to manganous ions in vitro did not explain the extent of infection they caused on wheat hosts. In a similar experiment four Australian wheat genotypes were grown in the same Mn-deficient calcareous sand and inoculated with one virulent isolate of Ggt. Two genotypes were inefficient at taking up manganese and were very susceptible to take-all, one was very efficient at taking up manganese and was resistant to take-all, and the fourth genotype was intermediate for both characters. All genotypes were equally resistant under Mn-adequate conditions.     

The effect of take-all disease on gas-exchange rates and biomass in two winter wheat lines with different drought response

There have been no studies of the effect of take-all on leaf gas-exchange rates, despite the fact that take-all severely restricts plant water and nutrient uptake, which results in significant biomass and grain yield reduction. Here we describe the effect of inoculation with Gaeumannomyces graminis (Sacc.) var. tritici (Ggt) on carbon assimilation rate (A) and biomass production of wheat plants grown under two water regimes. We show that the impact of Ggt inoculation on plant growth and leaf A may be through reduced photosynthetic capacity of the leaves and not water stress per se. The nature of this reduced photosynthetic capacity remains uncertain but may involve nutrient deficiency and different enzymes produced by the fungus. In each of the 3 years the experiment was conducted, Ggt significantly reduced A, i.e. at anthesis by 18% in 2000, 15% in 2001, and 12% in 2002. In agreement with other field studies, Ggt reduced tiller number and production of all plant components, mostly root dry mass and grain mass per plant. Highly significant negative correlations were found between disease rating and A in all years, showing that at disease ratings equal or higher than 3 (on a scale from 1 to 4) A could practically be zero. While A decreased, intercellular CO₂ concentration increased or did not change, and stomatal conductance was relatively high. In addition, A was more reduced under high than under low soil moisture content. These results support the idea that water stress per se did not contribute to the observed reduction of A. The mechanism of photosynthetic capacity reduction due to the Ggt root-rotting fungus is of interest as it may lead to the molecular mechanisms of plant resistance and ultimately to the development of take-all resistant plants.     

Natural suppression of take-all disease of wheat in Montana soils

This research was initiated to determine whether soils suppressive to take-all of wheat caused by Gaeumannomyces graminis var. tritici (Ggt) occur in Montana, and to identify the organisms most likely involved in this suppression. From an initial screening of eight soils collected from different wheat growing areas of Montana, two were highly suppressive to take-all. Microbial characterization of these soils indicated that different mechanisms were involved in the suppression. In Larslan soil, mycoparasitism appeared to be the main mechanism. Two different fungi with exceptional ability to reduce the severity of take-all were isolated from this soil. One of these fungi could parasitize the hyphae of Ggt. Field tests with these fungi in Ggt infested soil showed increases of over 100% in both harvestble tillers and grain yield as compared to treatments without these two fungi. In tests with 48 different bacteria and 10 actinomycetes from Larslan soil, none were able to consistently reduce severity of take-all alone, or in mixtures. In Toston soil, antibiosis by actinomycetes and perhaps the involvement of Pseudomonas spp. in production of antibiotics and/or siderophores appeared to be the most likely mechanisms involved in take-all suppression. Increases in shoot dry weight over that in the Ggt infested control using mixtures of pseudomonads and actinomycetes ranged from 25% to 87%. Actinomycetes added individually or in mixtures to soil infested with Ggt consistently reduced the severity of the disease to a greater extent than did mixtures of Pseudomonas spp.     

Evidence for the co-circulation of dengue virus type 3 genotypes III and V in the Northern region of Brazil during the 2002-2004 epidemics

The reintroduction of dengue virus type 3 (DENV-3) in Brazil in 2000 and its subsequent spread throughout the country was associated with genotype III viruses, the only DENV-3 genotype isolated in Brazil prior to 2002. We report here the co-circulation of two different DENV-3 genotypes in patients living in the Northern region of Brazil during the 2002-2004 epidemics. Complete genomic sequences of viral RNA were determined from these epidemics, and viruses belonging to genotypes V (Southeast Asia/South Pacific) and III were identified. This recent co-circulation of different DENV-3 genotypes in South America may have implications for pathological and epidemiological dynamics.     

Whitefly Bemisia tabaci (Homoptera: Aleyrodidae) infestation on cassava genotypes grown at different ecozones in Nigeria

Large-scale screening of cassava, Manihot esculenta Crantz, genotypes for resistance to infestation by whitefly Bemisia tabaci Gennadius, the vector of cassava mosaic geminiviruses, is limited. A range of new cassava elite clones were therefore assessed for the whitefly infestation in the 1999/2000 and 2000/2001 cropping seasons in experimental fields of International Institute of Tropical Agriculture, Ibadan, Nigeria. On each scoring day, between 0600 and 0800 hours when the whiteflies were relatively immobile, adult whitefly populations on the five topmost expanded leaves of cassava cultivars were counted. All through the 6-mo scoring period, there was a highly significant difference in whitefly infestation among the new cassava elite clones. Vector population buildup was observed in Ibadan (forest-savanna transition zone) and Onne (humid forest), 2 mo after planting (MAP). Mean infestation across cassava genotypes was significantly highest (16.6 whiteflies per plant) in Ibadan and lowest in Zaria (0.2). Generally, whitefly infestation was very low in all locations at 5 and 6 MAP. During this period, cassava genotypes 96/1439 and 91/02324 significantly supported higher infestations than other genotypes. Plants of 96/1089A and TMS 30572 supported the lowest whitefly infestation across cassava genotypes in all locations. The preferential whitefly visitation, the differences between locations in relation to whitefly population, cassava mosaic disease, and the fresh root yield of cassava genotypes are discussed.     

Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores

A nested multiplex PCR (polymerase chain reaction) approach was used for multilocus genotyping of arbuscular mycorrhizal fungal populations. This method allowed us to amplify multiple loci from Glomus single spores in a single PCR amplification. Variable introns in the two protein coding genes GmFOX2 and GmTOR2 were applied as codominant genetic markers together with the LSU rDNA. Genetic structure of Glomus spp. populations from an organically and a conventionally cultured field were compared by hierarchical sampling of spores from four plots in each field. Multilocus genotypes were characterized by SSCP (single stranded conformation polymorphism) and sequencing. All spore genotypes were unique suggesting that no recombination was taking place in the populations. There were no overall differences in the distribution of genotypes in the two fields and identical genotypes could be sampled from both fields. Analysis of gene diversity indicated that Glomus populations are subdivided between plots within each field. There were however, no subdivision between the fields.     

High level of polymorphism and spatial structure in a selfing plant species,Medicago truncatula (Leguminosae), shown using RAPD markers

Using RAPD markers and one morphological marker, we studied the among- and within-population structure in a selfing annual plant species, Medicago truncatula GAERTN. About 200 individuals, sampled from four populations subdivided into three subpopulations each, were scored for 22 markers. It was found that the within-population variance component accounted for 55% of the total variance, while the among-population variance component accounted for 45%. Eighteen percent of the total variance was due to within-population structure (i.e., among subpopulations). Thus, 37% of the total variance was within subpopulations. Using a multilocus approach, it was found that no multilocus genotype was common to two populations. Two of the four studied populations were composed of few (≤6) multilocus genotypes, whereas the other two had many (≥15) multilocus genotypes. In the most polymorphic population (37 genotypes), only one genotype was found to be common to two subpopulations. Resampling experiments show that, depending on the population, three to 16 polymorphic loci were necessary and sufficient to score all multilocus genotypes in the population. When these data are compared to published results, it appears that on some occasions, the number of genotypes per population of selfing species might be larger than would be expected from the sole consideration of effective population size. The large within-subpopulation genetic variance observed in some populations could be explained by either small neighborhood sizes within subpopulations, or by outcrossing following migration through seed and/or pollen.     

Historical and contemporary multilocus population structure of Ascochyta rabiei (teleomorph: Didymella rabiei) in the Pacific Northwest of the United States

The historical and contemporary population genetic structure of the chickpea Ascochyta blight pathogen, Ascochyta rabiei (teleomorph: Didymella rabiei), was determined in the US Pacific Northwest (PNW) using 17 putative AFLP loci, four genetically characterized, sequence-tagged microsatellite loci (STMS) and the mating type locus (MAT). A single multilocus genotype of A. rabiei (MAT1-1) was detected in 1983, which represented the first recorded appearance of Ascochyta blight of chickpea in the PNW. During the following year many additional alleles, including the other mating type allele (MAT1-2), were detected. By 1987, all alleles currently found in the PNW had been introduced. Highly significant genetic differentiation was detected among contemporary subpopulations from different hosts and geographical locations indicating restricted gene flow and/or genetic drift occurring within and among subpopulations and possible selection by host cultivar. Two distinct populations were inferred with high posterior probability which correlated to host of origin and date of sample using Bayesian model-based population structure analyses of multilocus genotypes. Allele frequencies, genotype distributions and population assignment probabilities were significantly different between the historical and contemporary samples of isolates and between isolates sampled from a resistance screening nursery and those sampled from commercial chickpea fields. A random mating model could not be rejected in any subpopulation, indicating the importance of the sexual stage of the fungus both as a source of primary inoculum for Ascochyta blight epidemics and potentially adaptive genotypic diversity.     

Interplay between ecological, behavioural and historical factors in shaping the genetic structure of sympatric walleye populations (Sander vitreus)

Disentangling ecological, behavioural and evolutionary factors responsible for the presence of stable population structure within wild populations has long been challenging to population geneticists. This study primarily aimed at decoding population structure of wild walleye (Sander vitreus) populations of Mistassini Lake (Québec, Canada) in order to define source populations to be used for the study of spatial partitioning using individual-based multilocus assignment methods, and decipher the dynamics of individual dispersal and resulting patterns of spatial resource partitioning and connectivity among populations. A second objective was to elucidate the relationships between biological characteristics (sex, size, age and population of origin) and an individual's probability to migrate and/or disperse. To do so, a total of 780 spawning individuals caught on five distinct spawning sites, and 1165 postspawning individuals, captured over two sampling seasons (2002-2003) were analysed by means of eight microsatellite loci. Four temporally stable walleye populations associated with distinct reproductive grounds were detected. These populations were differentially distributed among lake sectors during their feeding migration and their spatial distribution was stable over the two sampling seasons. Dispersing individuals were identified (n=61); these revealed asymmetrical patterns of dispersal between populations, which was also confirmed by divergent admixture proportions. Regression models underlined population of origin as the only factor explaining differential dispersal of individuals among populations. An analysis of covariance (ancova) indicated that larger individuals tended to migrate from their river of origin further away in the lake relative to smaller fish. In summary, this study underlined the relevance of using individual-based assignment methods for deciphering dynamics of connectivity among wild populations, especially regarding behavioural mechanisms such as differential spatial partitioning and dispersal responsible for the maintenance of genetic population structure.     

A Simulation Model for Assessing Soybean Rust Epidemics

A soybean rust (causal agent Phakopsora pachyrhizt) simulation model was developed for assessing disease epidemics as a part of pest risk analysis. Equations describing environmental effects on disease components were developed by re-analyzing previous data with a view toward a systems approach. The infection rate was predicted well using dew period and temperature after inoculation as independent variables (R²=0.88, P < 0.0001). The exponential models which used physiological day as an independent variable explained 98% of the variations of latent period and senescence of disease lesions. The simulation model was validated with data from 72 sequential planting experiments during 1980 and 1981 in Taiwan. Time of onset for these epidemics varied from 25—60 days and 50—80 days after planting soybean cultivars TK 5 and G 8587, respectively. The epidemic periods were 75—95 for TK 5 and 100—120 days for G 8587. Variation of epidemics was accurately predicted by the simulator. Predicted disease curves fit well the observed disease curves for the recognized cropping seasons, spring- and autumn-seeded crops. For G 8587, which is very sensitive to photoperiod, the data from spring and autumn gave a better fit compared with data from pre-summer planting. The model underestimated disease epidemics during the winter, probably because the plant growth model failed to reflect the photoperiod rection of soybean. The simulation model was validated with data from other experiments conducted in three cropping seasons in 1979 and 1980. Determination coefficients of the regression between observed and predicted disease severity were significant.     

Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78

Acinetobacter baumannii is an emerging opportunistic gram-negative pathogen responsible for hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant A. baumannii strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.     

Tracking pyrethroid resistance in the polyphagous bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae), in the shifting landscape of a cotton-growing area

In cotton-growing areas of Central Africa, timing of host crops and pest management practices in annual rainfed cropping systems result in a shifting mosaic of habitats that influence the dynamics and resistance of Helicoverpa armigera (Hübner) populations on spatial scales, both within and across seasons. From 2002 to 2006, regional and local resistance was monitored among cotton fields and among the major host plants of the bollworm. From 2002, pyrethroid resistance increased within and across cotton-growing seasons to reach a worrying situation at the end of the 2005 growing season. Cotton crops played a fundamental role in the increase in seasonal resistance, even if the intensive use of insecticides on local tomato crops strongly concentrated resistance alleles in residual populations throughout the off-season. Due to the relative stability of resistance in H. armigera populations despite a long off-season, we believe that after the dispersal of the moths southwards at the end of the growing season, reverse migration mainly accounts for the reconstitution of populations at the onset of the following growing season. In addition, local resistance monitoring in 2005 and 2006 showed that it was possible to control the increase in resistance by temporarily stopping the use of pyrethroids during the period of peak infestation of cotton by H. armigera. On the other hand, the similar resistance frequency of populations sampled from sprayed and unsprayed synchronous hosts confirmed the absence of reproductive isolation between adults. As a result, diversity in cropping systems should be encouraged by planting alternative host plants to provide a mosaic of habitats, which in return would provide insecticide-free refuges. The implications for insecticide resistance management in annual cropping systems are discussed.     

Molecular markers reveal differentiation among isolates of Coccidioides immitis from California, Arizona and Texas

Coccidioides immitis causes coccidioidomycosis, a fungal disease of both immunocompromised and otherwise healthy people; it is capable of causing large epidemics and the disease is often refractory to chemotherapy. To quantify the magnitude of population differentiation and estimate levels of gene flow in C. immitis , multilocus genotypes were scored for 20–25 clinical isolates from each of Bakersfield (California), Tucson (Arizona), and San Antonio (Texas). The molecular markers used were PCR products with polymorphic restriction endonuclease sites, found and characterized in a previous study of the Tucson population. The data show very highly significant differences in allele frequencies between all three populations, and suggest very low levels of migration between populations. One isolate in the San Antonio sample was an outlier, showing the California-specific allele at all four of the loci distinguishing the two populations, and subsequent inquiries indicated that the infection had indeed been acquired in California. Thus, genetic information can be used to infer the geographical origin of a fungal infection.     

Prediction of take-all disease risk in field soils using a rapid and quantitative DNA soil assay

A rapid, routine DNA-based assay to quantify Gaeumannomyces graminis var. tritici (Ggt), the causal agent of take-all disease of cereals, has been developed and used for the prediction of take-all in a wide range of field soils. Based on the correlation of the DNA-based assay and a soil bioassay, the risk of disease development can be estimated. Ggt DNA levels of <30 pg, 30–50 pg and >50 pg in 0.1 g soil organic matter correspond to low, moderate and high levels of the disease, respectively. Limitations in the prediction of take-all, including sampling requirements to obtain representative soil samples from fields and increasing the sensitivity and the accuracy of the DNA assay, are described. The main advantage in using the DNA-based assay, in estimating the amount of Ggt inoculum in soil, is that the levels of Ggt in soil samples can be assessed rapidly and accurately. Farmers can now have soil samples assessed before sowing. The DNA result can be used to predict the potential yield loss and determine the most appropriate management options using decision support software that is currently available. This DNA technology is currently being used commercially to detect and predict take-all. This revised version was published online in June 2006 with corrections to the Cover Date.     

Egg diapause and clonal structure in parthenogenetic populations of Heterocypris incongruens (Ostracoda)

A study of the clonal structure of parthenogenetic populations of Heterocypris incongruens from rice-fields in Northern Italy carried out over two-year period is summarized. Significantly different levels of genetic polymorphism were found among populations. The coexistence of different electrophoretic clones and similar patterns of clonal seasonal succession have been observed in at least two different rice fields. The clone or group of clones present in fall, winter and early spring is substituted by other multilocus genotypes in late spring and summer. Different egg diapause induction mechanisms drive the clonal substitution in different clones. Here we report a new laboratory experiment designed to test the effect of temperature and photoperiod found in winter (12 °C 8:16 L:D), spring (24°C 12:12 L:D) and summer (28°C 16:8 L:D) conditions on the deposition and hatching of diapausal eggs in different multilocus genotypes. Clones respond in a way compatible with their sustained presence in the field in different seasons.     

Comparative analysis of population characteristics of the brown planthopper,Nilaparvata lugens stål,between wet and dry rice cropping seasons in West Java,Indonesia

Population dynamics of the brown planthopper (BPH),Nilaparvata lugens Stål, were investigated in paddy fields in the coastal lowland of West Java, Indonesia, where rice is cultivated twice a year, in the wet and dry cropping seasons. Distinct differences in the basic features of population dynamics were detected between the two rice cropping seasons: (1) In the wet season, BPH populations multiplied rapidly in the period from initial to peak generation, reaching quite often the destructive level despite the low density of initial immigrants. However, in the dry season, the population growth rate and the peak population density were much lower than those in the wet season. The abundance of natural enemies such as arthropod predators played a major role in determining such a difference in seasonal population development. (2) The density at the peak generation or the occurrence of outbreaks in each field was predictable in the wet season with fairly high accuracy on the basis of the density at the initial or previous seasonal generations. In the dry season, however, the rate of population growth and the peak population density widely varied among the fields depending on the water status in each field. (3) Density-dependent processes to regulate the population density were detected in both cropping seasons. In the wet season, the regulatory processes were only detected in such high densities as cause the considerable deterioration of host plants, which suggested that the processes were largely attributable to intra-specific competition. In the dry season, however, the regulatory processes operated at a much lower density in the earlier stages of the crops. The results of an analysis of adult longevity or residence period suggested that the density-dependent dispersal of macropterous adults played an important role in stabilizing the population fluctuation among the fields in the early dry season.     

The microbiology of soils under successive wheat crops in relation to take-all disease

Abstract Thirty-eight wheat fields in southern England were sampled in an attempt to correlate the amount of take-all disease with 35 microbiological and chemical measurements of soil. There was little correlation between field take-all and pot tests to determine soil infectivity. Myxogastrids were important components of the soil population, being up to half of the amoebal population, and most soils contained dictyostelids, reticulate amoebae and myxobacteria. Amoebae, ciliates, bacteria and saprophytic fungi were recorded for all soils. pH was a major determinant of soil populations, being clearly correlated with fungal abundance and with numbers of ciliates, dictyostelids and bacteria. Principal component analysis separated dictyostelids from the other soil amoebae and again showed the importance of pH in determining soil microbial populations. Take-all was negatively correlated with soil fertility and positively related to nematodes and myxobacteria, but this was probably an effect of take-all, and represented saprophytic growth on dead roots rather than being a cause. Reticulate amoebae and dictyostelids were both correlated with low levels of take-all. This study emphasises the large number of interrelated populations of soil microorganisms which could have an effect on the severity of take-all infections.     

genecap: a program for analysis of multilocus genotype data for non‐invasive sampling and capture‐recapture population estimation

We created genecap to facilitate analysis of multilocus genotype data for use in non‐invasive DNA sampling and genetic capture‐recapture studies. genecap is a Microsoft excel macro that uses multilocus genetic data to match samples with identical genotypes, calculate frequency of alleles, identify sample genotypes that differ by one and two alleles, calculate probabilities of identity, and match probabilities for matching samples. genecap allows the user to include background data and samples with missing genotypes for multiple loci. Capture histories for each user‐defined sampling period are output in formats consistent with commonly employed population estimation programs.